Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctcgaatattttatttacatcaagggatcttagagttcatcttgaaaaataaaagagcagcttaggaacataaacattccttttttttacatcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAAAGGAGGGCCAGGATTCAACTAGAATCTGAAGCGAGGGAAGTGAACCCTT

Basic information

species Zea mays
transcript GRMZM2G130548_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130548_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os02g51290.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------------------cctcgaatattttatttacatcaagggatcttagagttcatcttgaaaaataaaagagcagcttaggaacataaacattcctttt----------ttttacatcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAAAGGAGGGCCAGGATTCAACTAGAATCTGAAGCGAGGGAAGTGAACCCTT
                                                              |||| | | |  | || || |||    ||    | |  | || | || ||| | ||   |  |        ||||           ||| |  || |||||||||||  ||| ||| |||||||||| ||||||||||||||||||| |||||| || |||| |  | |||||||| | ||||| ||||| | ||| ||||
gtattatctacttatggatccatttaaagttagaattcttctgtgaacagaagtagtcccctttttgtctcctgctagcgacctttctttttgggt-gtcatatcagagtgcaacctacttatgtgttttaatctttggcacataacatttcaattcatgcagTTTAAGGCTTCAAACACAAGGCGCTCCATTCTGGAGGAGGTAGAGGCTGAAAGAAGAGCCAAGGCTGAACTAGAAGCAGAAGCAAGGGATGAGAATCCTT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|67010741|gb|CO439490.1|CO439490
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGATGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|47961743|gb|CN844452.1|CN844452
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|58030053|gb|CX725480.1|CX725480
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACGAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|18649488|gb|BM498307.1|BM498307
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGNTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGCTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|18649240|gb|BM498059.1|BM498059
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         CTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGCTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|76292040|gb|DV031608.1|DV031608
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|101383449|gb|EB813780.1|EB813780
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTTTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|29945355|gb|CB815597.1|CB815597
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|91877108|gb|EB407065.1|EB407065
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|5439382|gb|AI820303.1|AI820303
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|211067668|gb|FL012968.1|FL012968
EST:     GTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATNCT-GTTAACAAG                         TTTAAGAGTTCGAACCCA-GGCGCTCAATTCTGGGAGAAG-TAGAGGTTGA
genomic: GTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAAT-CTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGG-AGGAGGTAGAGGTTGA
EST: gi|29945353|gb|CB815596.1|CB815596
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|60341409|gb|DN208382.1|DN208382
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|16926976|gb|BM080044.1|BM080044
EST:     GGGACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|211067665|gb|FL012965.1|FL012965
EST:     ACATTGAGCAAAATGGATCAAAAGCGTTTTGAGAATCNTTGTTAACCAAG                         TTTAAGAGTTCGAACCCAAGGCGCTC
genomic: ACATTGAGCAAAATGGATCAAAAGCGTTT-GAGAATC-TTGTTAAC-AAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTC
EST: gi|45567900|gb|CK985803.1|CK985803
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|32831864|gb|CD971542.1|CD971542
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTATGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|22489673|gb|BU049596.1|BU049596
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|18649960|gb|BM498779.1|BM498779
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|9732626|gb|BE511378.1|BE511378
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|87153170|gb|DY397959.1|DY397959
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|50337773|gb|CO532899.1|CO532899
EST:     GGTACATTGAGCAAAATGGATCANAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGA
EST: gi|211470172|gb|FL446046.1|FL446046
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAG-----TGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|211320303|gb|FL454022.1|FL454022
EST:     GGTACATTGAGCAAAATGGWTCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|91877109|gb|EB407066.1|EB407066
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAAACCCA-GGCGCTNCA-TTCTGGAGG
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAA-CCCAAGGCGCT-CAATTCTGGAGG
EST: gi|50337772|gb|CO532898.1|CO532898
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|32865321|gb|CF005003.1|CF005003
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|211067669|gb|FL012969.1|FL012969
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTGTGAG--TG--GT-AACAAG                         TTTAAGAGTTCGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAA
EST: gi|18450405|gb|BM428683.1|BM428683
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGCTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|211023896|gb|FL457615.1|FL457615
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
EST: gi|19822487|gb|BQ048511.1|BQ048511
EST:     GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAG                         TTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA
genomic: GGTACATTGAGCAAAATGGATCAAAAGCGTTTGAGAATCTTGTTAACAAGgtattatctg ... catcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaataaaagagcagcttaggaacataaacattccttttttttacatcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAAAGGAGGGCCAGGATTCAACTAGAATCTGAAGCGAGGGAAGTGAACCCTT
                                ttccttttttttacat  CT-rich tract
                               attcctttttttta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctcgaatattttatttacatcaagggatcttagagttcatcttgaaaaataaaagagcagcttaggaacataaacattccttttttttacatcgtgcagTTTAAGAGTTCGAACCCAAGGCGCTCAATTCTGGAGGAGGTAGAGGTTGAAAGGAGGGCCAGGATTCAACTAGAATCTGAAGCGAGGGAAGTGAACCCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC